Merge pull request #1193 from pints-team/i208-pip

i208 pip

.github/workflows/upload-to-pypi.yml

@@ -0,0 +1,36 @@
+name: Upload to PyPi
+
+on:
+  release:
+    types:
+      - published
+
+jobs:
+
+  upload-to-pypi:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v1
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.8
+          architecture: x64
+
+      - name: install dependencies
+        run: |
+          python --version
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install --upgrade twine
+
+      - name: create release binaries
+        run: |
+          python setup.py sdist bdist_wheel
+
+      - name: publish to PyPI
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}

.gitignore

@@ -27,3 +27,7 @@ studies
 
 # Virtual environments
 venv*
+
+# Build artifacts
+build/*
+dist/*

README.md

@@ -1,8 +1,8 @@
 [![Unit tests on multiple python versions](https://github.com/pints-team/pints/workflows/Unit%20tests%20on%20multiple%20python%20versions/badge.svg)](https://github.com/pints-team/pints/actions)
 [![Unit tests on multiple operating systems](https://github.com/pints-team/pints/workflows/Unit%20tests%20on%20multiple%20operating%20systems/badge.svg)](https://github.com/pints-team/pints/actions)
 [![codecov](https://codecov.io/gh/pints-team/pints/branch/master/graph/badge.svg)](https://codecov.io/gh/pints-team/pints)
-[![Functional testing code](https://github.com/pints-team/functional-testing/blob/master/badge-code.svg)](https://github.com/pints-team/functional-testing)
-[![Functional testing results](https://github.com/pints-team/functional-testing/blob/master/badge-results.svg)](https://www.cs.ox.ac.uk/projects/PINTS/functional-testing)
+[![Functional testing code](https://raw.githubusercontent.com/pints-team/functional-testing/master/badge-code.svg)](https://github.com/pints-team/functional-testing)
+[![Functional testing results](https://raw.githubusercontent.com/pints-team/functional-testing/master/badge-results.svg)](https://www.cs.ox.ac.uk/projects/PINTS/functional-testing)
 [![binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/pints-team/pints/master?filepath=examples)
 [![readthedocs](https://readthedocs.org/projects/pints/badge/?version=latest)](http://pints.readthedocs.io/en/latest/?badge=latest)
 [![BCH compliance](https://bettercodehub.com/edge/badge/pints-team/pints?branch=master)](https://bettercodehub.com/results/pints-team/pints)
@@ -11,8 +11,8 @@
 
 PINTS (Probabilistic Inference on Noisy Time-Series) is a framework for optimisation and Bayesian inference on ODE models of noisy time-series, such as arise in electrochemistry and cardiac electrophysiology.
 
-PINTS is described in [this publication in JORS](http://doi.org/10.5334/jors.252), and can be cited using the information given in our [CITATION file](./CITATION).
-More information about PINTS papers can be found in the [papers directory](./papers/).
+PINTS is described in [this publication in JORS](http://doi.org/10.5334/jors.252), and can be cited using the information given in our [CITATION file](https://github.com/pints-team/pints/blob/master/CITATION).
+More information about PINTS papers can be found in the [papers directory](https://github.com/pints-team/pints/tree/master/papers).
 
 
 ## Using PINTS
@@ -28,19 +28,19 @@ simulate(parameters, times) --> Returns a vector of model evaluations at
 ```
 
 Experimental data sets in PINTS are defined simply as lists (or arrays) of `times` and corresponding experimental `values`.
-If you have this kind of data, and if [your model (or model wrapper)](examples/writing-a-model.ipynb) implements the two methods above, then you are ready to start using PINTS to infer parameter values using [optimisation](examples/optimisation-first-example.ipynb) or [sampling](examples/sampling-first-example.ipynb).
+If you have this kind of data, and if [your model (or model wrapper)](https://github.com/pints-team/pints/blob/master/examples/stats/custom-model.ipynb) implements the two methods above, then you are ready to start using PINTS to infer parameter values using [optimisation](https://github.com/pints-team/pints/blob/master/examples/optimisation/first-example.ipynb) or [sampling](https://github.com/pints-team/pints/blob/master/examples/sampling/first-example.ipynb).
 
 A brief example is shown below:  
-![An example of using PINTS in an optimisation](example.svg)  
+![An example of using PINTS in an optimisation](https://raw.githubusercontent.com/pints-team/pints/f2e28d09a2668f883a7358ae7aaad4b4572554eb/example.svg)  
 _(Left)_ A noisy experimental time series and a computational forward model.
 _(Right)_ Example code for an optimisation problem.
-The full code can be [viewed here](examples/readme-example.ipynb) but a friendlier, more elaborate, introduction can be found on the [examples page](examples/README.md).
+The full code can be [viewed here](https://github.com/pints-team/pints/blob/master/examples/sampling/readme-example.ipynb) but a friendlier, more elaborate, introduction can be found on the [examples page](https://github.com/pints-team/pints/blob/master/examples/README.md).
 
 A graphical overview of the methods included in PINTS can be [viewed here](https://pints-team.github.io/pints-methods-overview/).
 
 ### Examples and documentation
 
-PINTS comes with a number of [detailed examples](examples/README.md), hosted here on github.
+PINTS comes with a number of [detailed examples](https://github.com/pints-team/pints/blob/master/examples/README.md), hosted here on github.
 In addition, there is a [full API documentation](http://pints.readthedocs.io/en/latest/), hosted on readthedocs.io.
 
 
@@ -60,12 +60,14 @@ $ pip install --upgrade pip
 Then navigate to the path where you downloaded PINTS to, and install both PINTS and its dependencies by typing:
 
 ```
-$ pip install .
+$ pip install pints
 ```
 
-To install PINTS as a [developer](CONTRIBUTING.md), use
+To install PINTS as a [developer](https://github.com/pints-team/pints/blob/master/CONTRIBUTING.md), use
 
 ```
+$ git clone https://github.com/pints-team/pints.git
+$ cd pints
 $ pip install -e .[dev,docs]
 ```
 
@@ -77,11 +79,11 @@ $ pip uninstall pints
 
 ## Contributing to PINTS
 
-If you'd like to help us develop PINTS by adding new methods, writing documentation, or fixing embarassing bugs, please have a look at these [guidelines](CONTRIBUTING.md) first.
+If you'd like to help us develop PINTS by adding new methods, writing documentation, or fixing embarassing bugs, please have a look at these [guidelines](https://github.com/pints-team/pints/blob/master/CONTRIBUTING.md) first.
 
 ## License
 
-PINTS is fully open source. For more information about its license, see [LICENSE](LICENSE.md).
+PINTS is fully open source. For more information about its license, see [LICENSE](https://github.com/pints-team/pints/blob/master/LICENSE.md).
 
 ## Get in touch
 

pints/version

@@ -1 +1 @@
-0,2,2
+0,3,0

setup.py

@@ -34,6 +34,7 @@ def load_version():
     # Description
     description='Probabilistic Inference in Noisy Time-Series',
     long_description=readme,
+    long_description_content_type='text/markdown',
 
     # License name
     license='BSD 3-clause license',
@@ -73,4 +74,5 @@ def load_version():
             'traitlets',
         ],
     },
+    python_requires='>=2.7,!=3.0,!=3.1,!=3.2,!=3.3,!=3.4',
 )